Research in my lab centers on the role of soil microorganisms in impacting plant growth, physiology, and fitness. We apply concepts and techniques in microbial ecology to uncover the relationships between soil microbial communities and plant traits. The research projects include the use of experimental microbial ecosystems to uncover the microbial-based mechanisms mediating plant and ecosystem traits. Examining the mechanistic basis of microbial selection studies can yield the development of microbial consortia, isolation of new microbial strains, and purification of compounds that enhance desirable plant populations while suppressing weeds. For more information, visit my lab website.
My extension duties focus on assisting public and private audiences with the most appropriate methods to manage weedy and invasive plants in horticultural landscapes. We are developing a web-based software program that allows users to select weed control methods based on conventional or organic weed management preferences. We work with public, private, and university partners in developing innovative, cost-effective control strategies that can be integrated into sustainable weed management programs. My outreach websites include:
Gannett, M., DiTommaso, A., Sparks, J. P., and J. Kao-Kniffin*. 2025. Microbial nitrogen immobilization reduces competitive advantage of nitrophilous plants with soybean. Plant and Soil. 508(1): 819-838. DOI:10.1007/s11104-024-06830-4
Liao, C., Kao-Kniffin, J., Reid, M., Zhu, W., Tshabalalah, P., LaPoint, J. Butler-Jones, Z., Pereira, A., Butler, N., Yu, T., and S. McCouch. 2025. Rice farming for climate change adaptation in the northeastern United States. PNAS. In press.
Son, Y., He, P., Craft, E. J., Piñeros, M. A., Baldwin, M., Wang, Z. Gu, A., and J. Kao-Kniffin*. 2025. Synergistic enhancement of Sorghum bicolor nutrient uptake and growth by EBPR microbiomes and AM fungi. Environmental Microbiome. In press.
Son, Y., He, P., Baldwin, M., Li, G., Wang, Z., Gu, A. Z., and J. Kao-Kniffin*. 2025. Geno-pheno characterization of crop rhizospheres: An integrated Raman spectroscopy and microbiome approach in conventional and organic agriculture. Frontiers in Microbiology. In press.
Xiao, J., Kao‐Kniffin, J., and B. Zhu 2025. Arbuscular mycorrhizal fungi enhance nitrogen acquisition from, but not carbon loss of, organic matter in soil. New Phytologist. 247(3): 1415-1425. DOI:10.1111/nph.70274
Lane, C., Kao-Kniffin, J., and C. Watkins. 2025. Packing line processes reshape apple microbiomes: Differential effects of chlorine and waxing on bacterial and fungal communities. HortScience. DOI:10.21273/HORTSCI18722-25
Wang, Z., Han, I. L., Lee, J., Li, G., He, P., Baldwin, M. T., Kao-Kniffin, J., Wu, L., Zhou, J., and A. Z. Gu. 2025. Climate warming enhances biodiversity and stability of grassland soil phosphorus-cycling microbial communities. The ISME Journal. wraf118. DOI:1093/ismejo/wraf118
Jernigan, A. B., Kao-Kniffin, J., Pethybridge, S., Sosnoskie, L., and K. Wickings. 2025. Common soil invertebrate (Collembola: Isotomiella minor) reduces weed biomass and alters weed communities. Applied Soil Ecology. 212, 106178. DOI:10.1016/j.apsoil.2025.106178
Chou, M. Y., Patil, A. T., Huo, D., Lei, Q., Kao-Kniffin, J., and P. Koch. 2025. Fungicide use intensity influences the soil microbiome and links to fungal disease suppressiveness in amenity turfgrass. Applied and Environmental Microbiology. e01771-24. DOI:10.1128/aem.01771-24
He, P., Son, Y., Berkowitz, J., Li, G., Lee, J., Han, I. L., Craft, E., Pineros, M, Kao-Kniffin, J., and A.Z. Gu. 2025. Recycled phosphorus bioamendments from wastewater impact rhizomicrobiome and benefit crop growth: Sustainability implications at water-food nexus. Environmental Science & Technology. DOI:10.1021/acs.est.4c07901
Lane, C., Shoffe, Y., Brown, M., Cheng, L., Kao-Kniffin, J., Peck, G., Dandekar, A., and C. Watkins. 2025. Reduced sorbitol genotype alters postharvest microbiomes of ‘Greensleeves’ apples." Journal of the American Society for Horticultural Science. 150(5): 279-289. DOI: 10.21273/JASHS05521-25
- Gannett, M., DiTommaso, A., Sparks, J.P., and J. Kao-Kniffin*. 2024. Microbial nitrogen immobilization as a tool to manage weeds in agroecosystems. Agriculture, Ecosystems & Environment, 366, 108904. DOI: https://doi.org/10.1016/j.agee.2024.108904.
- Garcia, J., Bray, N., Son, Y., Butler-Jones, A., and J. Kao-Kniffin*. 2023. Plant growth and microbial responses from urban agriculture soils amended with excavated local sediments and municipal composts. Journal of Urban Ecology, 9(1), juad016. DOI: https://doi.org/10.1093/jue/juad016.
- Groffman, P. M., Suchy, A. K., Locke, D.H., Johnston, R.J., Newburn, D.A., Gold, A.J., Band, L.E., Duncan, J., Grove, J.M., Kao-Kniffin, J. and H. Meltzer. 2023. Hydro-bio-geo-socio-chemical interactions and the sustainability of residential landscapes. PNAS Nexus, 2(10), pgad316. DOI: https://doi.org/10.1093/pnasnexus/pgad316.
- Lane, C., Al Shoffe, Y., Kao-Kniffin, J., and C.B. Watkins. 2023. Aminoethoxyvinylglycine and low oxygen controlled atmosphere storage shift functional microbiomes of ‘Gala’apples. Postharvest Biology and Technology, 206, 112546. DOI: https://doi.org/10.1016/j.postharvbio.2023.112546.
- Thompson, G., Bray, N., Groffman, P.M., and J. Kao-Kniffin*. 2023. Soil microbiomes in lawns reveal land-use legacy impacts on urban landscapes. Oecologia. 202, 337–351 DOI: https://doi.org/10.1007/s00442-023-05389-8.
- Jernigan, A., Kao-Kniffin, J., Pethybridge, S., and K. Wickings. 2023. Soil microarthropod effects on plant growth and development. Plant and Soil, 483: 27–45. DOI: https://doi.org/10.1007/s11104-022-05766-x
- Dastogeer, K.M.G, Kao-Kniffin, J., and S. Okazaki. Editorial: Plant microbiome: Diversity, functions, and applications. 2022. Front Microbiol. Sep 26;13:1039212. DOI: 10.3389/fmicb.2022.1039212.
- Garcia, J., M. Gannett, L. Wei, L. Cheng, S. Hu, J. Sparks, J. Giovannoni, and J. Kao-Kniffin*. 2022. Selection pressure on the rhizosphere microbiome can alter nitrogen use efficiency and seed yield in Brassica rapa. Communications Biology, 5(1): 959. DOI: https://doi.org/10.1038/s42003-022-03860-5
- King, W. L., Kaminsky, L. M., Gannett, M., Thompson, G. L., Kao‐Kniffin, J., and T. Bell. 2022. Soil salinization accelerates microbiome stabilization in iterative selections for plant performance. New Phytologist, 234(6), 2101-2110. DOI: https://doi.org/10.1111/nph.17774
- Cheng, L., A. DiTommaso, and J. Kao-Kniffin*. 2022. Opportunities for microbiome suppression of weeds using regenerative agricultural technologies. Frontiers in Soil Science. 2:838595. DOI: 10.3389/fsoil.2022.838595
- Parikh, T., S. P. Egendorf, I. Murray, A. Jamali, B. Yee, S. Lin, K. Cooper-Smith, B. Parker, K. Smiley, and J. Kao-Kniffin*. 2022. Greening the virtual smart city: Accelerating peer-to-peer learning in urban agriculture with virtual reality environments. Frontiers in Sustainable Cities. 3: 815937. DOI: https://doi.org/10.3389/frsc.2021.815937
- Gannett, M., N. Bray, J. Lampman, J. Lerner, K. Murray, V. Wallace, T. Yeh, M. Slavens, G.L. Thompson, and J. Kao-Kniffin*. 2021. Repetitive overseeding for ecological management of grass playing fields. HortScience. 56: 226-233. DOI: https://doi.org/10.21273/HORTSCI15419-20.
- Panke-Buisse K., L. Cheng, H. Gan, K. Wickings, M. Petrovic, and J. Kao-Kniffin*. 2020. Root fungal endophytes and microbial extracellular enzyme activities show patterned responses in tall fescues under drought conditions. Agronomy. 10(8):1076. https://doi.org/10.3390/agronomy10081076
- Howard, M.M., J. Kao‐Kniffin, and A. Kessler. 2020. Shifts in plant‐microbe interactions over community succession and their effects on plant resistance to herbivores. New Phytologist. 226, no. 4 (2020): 1144-1157 DOI: https://doi.org/10.1111/nph.16430
- Howard, M.M., C.A. Muñoz, J. Kao-Kniffin, and A. Kessler. 2020. Soil microbiomes from fallow fields have species-specific effects on crop growth and pest resistance. Frontiers in Plant Science. 11: 1171. DOI: https://doi.org/10.3389%2Ffpls.2020.01171.
- Bray, N., Thompson, G.L., Fahey, T., Kao-Kniffin, J., and Wickings, K. 2020.Soil macroinvertebrates alter the fate of root and rhizosphere carbon and nitrogen in a turfgrass lawn. Soil Biology and Biochemistry. 148: 107903. DOI:10.1016/j.soilbio.2020.107903
- Garcia, J. and J. Kao‐Kniffin*. 2020. Can dynamic network modeling be used to identify adaptive microbiomes? Functional Ecology. 34: 2065– 2074. https://doi.org/10.1111/1365-2435.13491
- Thompson, G.L. and J. Kao-Kniffin*. 2019 Urban grassland management implications for soil C and N dynamics: A microbial perspective. Frontiers in Ecology & Evolution, 7:315. DOI:10.3389/fevo.2019.00315
- Bray, N., Kao-Kniffin, J., Frey, S.D., Fahey, T., and K. Wickings. 2019. Soil macroinvertebrate presence alters microbial community composition and activity in the rhizosphere. Frontiers in Microbiology, 10:256. DOI: 10.3389/fmicb.2019.00256
- Kaminsky, L.M., G.L. Thompson, R.V. Trexler, T.H. Bell†*, and J. Kao-Kniffin†. 2019. Medicago sativa has reduced biomass and nodulation when grown with soil microbiomes conditioned to high phosphorous inputs. Phytobiomes, 2:237-248. DOI: https://doi.org/10.1094/PBIOMES-06-18-0025-R
